There is definately some repair code for buildings and other stuff that I wrote a decade or more back that cures the problem if you load a game from the save file. Multi hex buildings were always a problem from the SSI days on, and we have been fixing them like forever it seems...
It will likely require a small fix to the code that rubbles buildings which seems to be placing a rough hex there sometimes, either that or simply perhaps by calling the map repair code at the end of the player and/or AI phase, or the bombardment phase since it only seems to happen with arty terrain "modification"
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I may try bombarding a test multi hex building with an SU-152 in direct fire mode and see if blowing the registration hex to blazes with that mode of fire also shows the problem - it would be far simpler for testing than randomly pounding the ground with all the heavy artillery of a corps to see the effect.